+Open data
-Basic information
Entry | Database: PDB / ID: 8fcf | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of PLVAP CC1 in I212121 space group | |||||||||||||||
Components | Plasmalemma vesicle-associated protein | |||||||||||||||
Keywords | MEMBRANE PROTEIN / Endothelial cell-specific membrane protein / endothelial fenestrae / microvascular permeability | |||||||||||||||
Function / homology | Function and homology information positive regulation of cellular extravasation / developmental process / regulation of vascular permeability / tumor necrosis factor-mediated signaling pathway / caveola / MAPK cascade / perinuclear region of cytoplasm / cell surface / membrane / identical protein binding Similarity search - Function | |||||||||||||||
Biological species | Mus musculus (house mouse) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||||||||
Authors | Chang, T.H. / Hsieh, F.L. / Gu, X. / Kavran, J. / Gabelli, S.B. / Nathans, J. | |||||||||||||||
Funding support | United States, France, 4items
| |||||||||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae. Authors: Chang, T.H. / Hsieh, F.L. / Gu, X. / Smallwood, P.M. / Kavran, J.M. / Gabelli, S.B. / Nathans, J. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8fcf.cif.gz | 139.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8fcf.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 8fcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/8fcf ftp://data.pdbj.org/pub/pdb/validation_reports/fc/8fcf | HTTPS FTP |
---|
-Related structure data
Related structure data | 8fbyC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 10793.318 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plvap, Pv1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91VC4 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.93 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate, pH 5.0 and 15% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→39.928 Å / Num. obs: 14322 / % possible obs: 92 % / Redundancy: 12.1 % / CC1/2: 0.995 / Rpim(I) all: 0.041 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.95→2.05 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 753 / CC1/2: 0.8075 / Rpim(I) all: 0.329 / % possible all: 88 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→39.93 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.889 / SU R Cruickshank DPI: 0.341 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.227 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.19
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.23 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.41 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.95→39.93 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.95→2.11 Å / Total num. of bins used: 7
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|